On my Model S, I placed an angled Qi charging stand in the front of the adjustable cupholder area at the base of the console, and shifted the cupholders sides a few notches back. I was able to route the USB cable from the USB ports under the built-in charging dock (which has the Lightning connector for my wife's iPhone) same as the wires are routed for the built-in dock, but just continue the cable forward into the cupholder area since they are not partitioned off underneath. A Qi stand with a circular base worked best since half a cupholder wall nestles it in that spot - made for a clean though not quite built-in solution.
Unfortunately the Model 3 doesn't have that adjustable cupholder area; but perhaps just a wafer-thin Qi charging coil could be placed against the back of the built-in dock area....